############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL h5mread ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘h5mread’ ... ** this is package ‘h5mread’ version ‘0.99.4’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c H5File.c -o H5File.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c global_errmsg_buf.c -o global_errmsg_buf.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c H5DSetDescriptor.c -o H5DSetDescriptor.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c h5dimscales.c -o h5dimscales.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c uaselection.c -o uaselection.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c h5mread_helpers.c -o h5mread_helpers.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c h5mread_startscounts.c -o h5mread_startscounts.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c TouchedChunks.c -o TouchedChunks.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c h5mread_index.c -o h5mread_index.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c h5mread_sparse.c -o h5mread_sparse.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c h5mread.c -o h5mread.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c h5summarize.c -o h5summarize.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c R_init_h5mread.c -o R_init_h5mread.o gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o h5mread.so S4Vectors_stubs.o H5File.o global_errmsg_buf.o H5DSetDescriptor.o h5dimscales.o uaselection.o h5mread_helpers.o h5mread_startscounts.o TouchedChunks.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o R_init_h5mread.o /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/lib/libhdf5_hl.a /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-h5mread/00new/h5mread/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (h5mread)